title: Array 80, Heifer 3541, Fasted

description: Out of 51 Fasted, biological replicate 34


title: Array 82, Heifer 3585, Fasted

status: Public on May 20 2009

type: RNA

city: Guelph

first: John

middle: Henry

last: Doelman

state: Ontario

address: 50 Stone Road East

department: Animal and Poultry Science

country: Canada

institute: University of Guelph

description: Out of 51 Fasted, biological replicate 35

hyb_protocol: Labeled reference cDNA was mixed with labeled sample cDNA and hybridized to the array. Hybridizations were performed with a GeneTAC HybStation (Genomic Solutions, Ann Arbor, MI) using an 18 hour step-down hybridization protocol consisting of 3 six hour periods of 42°C, 35°C and 30°C, respectively

scan_protocol: Micorarrays were scanned and quantified using a Genepix 4200A axon scanner (Axon Instruments, Union City, USA)

data_processing: Microarrays were processed using Gene Pix Pro 6.0 (Axon Instruments, Inc., CA). Gene Spring GX (Agilent Technologies, Santa Rosa, CA) analysis software was used for LOWESS normalization procedures and statistical analysis (ANOVA, P = 0.05).

label: Alexa Fluor 555

molecule: total RNA

organism: Bos taurus

source_name: Liver, fasted 24 hours

label_protocol: SuperScript Indirect cDNA Labeling System (Invitrogen, Burlington, ON) was used to generate Alexa Fluor 555 or Alexa Fluor 647 labeled cDNA from ~20ug RNA

growth_protocol: Heifers were kept in group housing with 5 heifers per pen and grouped according to age.  They were all fed a forage based heifer total mixed ration once daily

extract_protocol: Total RNA extracted using TRI Reagent and Qiagen RNeasy Midi Kit.  Manufacturer's instructions were followed for both RNA extraction protocols.

treatment_protocol: Heifers were randomly assigned to pens, and pens were randomly assigned the fed (control) or fasted treatment. Heifers assigned to the fasted treatment were withheld feed the morning prior to scheduled liver biopsy. Liver biopsies were conducted when the average age of the pen was 12 months of age.

tag: gender

value: Female

tag: stage of development

value: Postpubertal; unbred

tag: tissue

value: Liver

label: Alexa Fluor 647

source_name: Bovine liver, spleen, and placenta

value: Spleen

value: Placenta

tag: stage of maturity

value: Lactating; mature


title: Array 49, Heifer 3559, Fasted

description: Out of 51 Fasted, biological replicate 29


title: Array 51, Heifer 3429, Fasted

description: Out of 51 Fasted, biological replicate 30


title: Array 87, Heifer 3571, Fasted

description: Out of 51 Fasted, biological replicate 36


title: Array 97, Heifer 3567, Fasted

description: Out of 51 Fasted, biological replicate 42


title: Array 48, Heifer 3460, Fasted

description: Out of 51 Fasted, biological replicate 28


title: Array 38, Heifer 3557, Fasted

description: Out of 51 Fasted, biological replicate 21


title: Array 89, Heifer 3476, Fasted

description: Out of 51 Fasted, biological replicate 38


title: Array 42, Heifer 3541, Fasted

description: Out of 51 Fasted, biological replicate 24


title: Array 65, Heifer 3536, Fasted

description: Out of 51 Fasted, biological replicate 32


title: Array 64, Heifer 3581, Fasted

description: Out of 51 Fasted, biological replicate 31


title: Array 45, Heifer 3499, Fasted

description: Out of 51 Fasted, biological replicate 26


title: Array 40, Heifer 3574, Fasted

description: Out of 51 Fasted, biological replicate 22


title: Array 37, Heifer 3563, Fasted

description: Out of 51 Fasted, biological replicate 20


title: Array 43, Heifer 3565, Fasted

description: Out of 51 Fasted, biological replicate 25


title: Array 41, Heifer 3549, Fasted

description: Out of 51 Fasted, biological replicate 23


title: Array 46, Heifer 3492, Fasted

description: Out of 51 Fasted, biological replicate 27


title: Array 78, Heifer 3593, Fasted

description: Out of 51 Fasted, biological replicate 33


title: Array 32, Heifer 3534, Fasted

description: Out of 51 Fasted, biological replicate 17


title: Array 33, Heifer 3527, Fasted

description: Out of 51 Fasted, biological replicate 18


title: Array 21, Heifer 3497, Fasted

description: Out of 51 Fasted, biological replicate 11


title: Array 29, Heifer 3522, Fasted

description: Out of 51 Fasted, biological replicate 16


title: Array 22, Heifer 3470, Fasted

description: Out of 51 Fasted, biological replicate 12


title: Array 23, Heifer 3515, Fasted

description: Out of 51 Fasted, biological replicate 13


title: Array 34, Heifer 3540, Fasted

description: Out of 51 Fasted, biological replicate 19


title: Array 27, Heifer 3513, Fasted

description: Out of 51 Fasted, biological replicate 15


title: F.candida_Phenanthrene_EC10_3

status: Public on May 21 2009

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: No additional information available.

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma (2.9.1) package in the R (2.4.0) software environment (http://www.r-project.org/), which consisted of Edward’s background correction (set off = 30) and global loess normalization. For each channel the median background intensity was substracted from the mean signal (foreground) intensity.

organism: Folsomia candida

source_name: Phenanthrene soil EC10 exposure

label_protocol: 500 ng input was used for amplification and labeling with the Agilent Low-Input Fluorescent Linear Amplification Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with phenanthrene EC10 (24.95 mg/kg (DW)).

source_name: Reference soil exposure (control)

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing control (reference) LUFA 2.2 soil (non-spiked).


title: Array 26, Heifer 3518, Fasted

description: Out of 51 Fasted, biological replicate 14


title: Array 20, Heifer 3488, Fasted

description: Out of 51 Fasted, biological replicate 10


title: Array 19, Heifer 3511, Fasted

description: Out of 51 Fasted, biological replicate 9


title: Array 14, Heifer 3501, Fasted

description: Out of 51 Fasted, biological replicate 8


title: Array 8, Heifer 3472, Fasted

description: Out of 51 Fasted, biological replicate 6


title: Array 6, Heifer 3465, Fasted

description: Out of 51 Fasted, biological replicate 5


title: Array 5, Heifer 3445, Fasted

description: Out of 51 Fasted, biological replicate 4


title: Array 2, Heifer 3405, Fasted

description: Out of 51 Fasted, biological replicate 2


title: Array 1, Heifer 3407, Fasted

description: Out of 51 Fasted, biological replicate 1


title: Array 3, Heifer 3438, Fasted

description: Out of 51 Fasted, biological replicate 3


title: Array 12, Heifer 3507, Fasted

description: Out of 51 Fasted, biological replicate 7


title: NF-3_cy3

type: genomic

city: Cardiff

first: Kiran

middle: Kumar

last: Mantripragada

address: Heath Park Campus

department: Medical Genetics

country: United Kingdom

institute: Cardiff University

hyb_protocol: The 32K slides were prehybridized in 5x SCC, 0.1% SDS at 45 ºC for at least one hour, washed with ddH20 and dried using compressed dust-free air. The dried pellets from the labeling steps were re-suspended in 50 µl of hybridization solution (50% Formamide, 4% SDS, 10 %, Dextran Sulfate, M.W. 500 000, 2 X SSC) and denatured for 5 min at 95°C, followed by incubation at 45°C for 2 h to block repetitive sequences. Subsequently, the probe mixture was applied to the slide surface, covered with a lifterslip (22x60mm, Erie Scientific, Portsmouth, NH) and hybridized at 45 °C for 20 hours in a slide chamber (Corning Inc. Life Sciences, Big Flats, NY). After hybridization the lifterslip was rinsed off using 1xPBS. Washing was performed in 25 % formamide, 2 X SSC, 0.1% SDS, at 45ºC, for 15 min, followed by 10 min in 1 X PBS at room temperature, and brief rinse in 0.2 X SSC. The array was immersed in deionized H2O and immediately dried using pressurized dust-free air.

scan_protocol: Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc, Union City, CA), and image analysis was carried out using the GenePixPro v6 software (Axon Instruments).

data_processing: We uploaded the GPR files from GenePix pro into a perl script called colloactor. This script links the information about clones to the array position. It also uploads the raw data to the BASE platform. These raw data files are attached as tables. Filtering and normalization was done using the LCB Data-WareHouse (dw.lcb.uu.se). The filters applied on the raw data removed spots containing more than 5% oversaturated pixels, spots with low Signal-to-Noise Ratio (SNR<3) and spots automatically and manually flagged as bad, absent or not found in GenePixPro program. Normalization was done using a print-tip loess method.

molecule: genomic DNA

organism: Homo sapiens

source_name: Neurofibroma

label_protocol: Two micrograms DNA was labelled using CY3 dCTP and CY5 dCTP (PA53021 and PA55021 respectively, GE Healthcare, Piscataway, NJ) according to the BioPrime® Array CGH Genomic Labeling System protocol (Invitrogen, Carlsbad, CA).The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vaccum centrifuge.

extract_protocol: genomic DNA isolation with phenol extraction according to standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989)

tag: disease state

value: neurofibroma

source_name: Peripheral blood derived DNA

value: Peripheral blood derived DNA

value: normal


title: NF-2_cy3


title: MPNST-23_cy3

source_name: MPNST

value: malignant peripheral nerve sheath tumours

value: malignant tumor

value: peripheral blood


title: NF-1_cy3.txt


title: MPNST-21_cy3


title: MPNST-24_cy3


title: MPNST-20_cy3


title: MPNST-22_cy3


title: AM- Scrotum4- AZA, 10nM DHT (Type 2)-1

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70768.gif
Compound Based Treatment: AZA,DHT
Cell Line: normal scrotum

hyb_protocol: Competitive hybridizations of Cy5 and Cy3 labeled probes on a total of 16 microarrays were performed for 14-18 hours over night at 65C in a water bath. Hybridized and washed microarrays were scanned using a Genepix 4000B microarray scanner (Axon, Foster City, USA). Images were analyzed with GenePix Pro 4.0 software (Axon Instruments, Foster City, USA).

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.08; Parameter Scan Time = 13:30:50; Parameter PMT Volts = 530; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20851; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.08; Parameter Scan Time = 13:30:50; Parameter PMT Volts = 560; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20927; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.03; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

data_processing: Only spots with fluorescence signals of > 1.5-fold over array background in either the experimental (Cy5) or the reference (Cy3) channel were considered based on the 16 microarray experiments representing the four experimental conditions corresponding to the four used cell strains in the first set of treatments. Cy5/Cy3 fluorescence ratios for all genes were normalized to obtain an average absolute log2 red / green ratio of 0 in each microarray. Fluorescence ratios for each gene were centered (by mean) and genes with at least 80% interpretable data in the microarrays were used. We further considered only those transcripts whose log2 red (Cy5) / green (Cy3) ratio differed from the mean expression level across all 16 experiments by at least 1.0 (corresponding to 2-fold up - or 2-fold down-regulation) in at least four of 16 experiments.

source_name: universal reference RNA

label_protocol: Spotted cDNA microarrays (Stanford Functional Genomics Facility, Stanford, CA, USA) were used for gene expression studies containing approximately 43,000 features representing 32,968 unique human genes. Labeling of aRNA and subsequent cDNA hybridizations were performed according to published protocols (http://cmgm.stanford.edu/pbrown/protocols/index.html). While 3 ug of each fibroblast aRNA was labeled with Cy5 (pseudocolor red), 2 microg of a universal human reference RNA was labeled with Cy3 (pseudocolor green) (Amersham Pharmacia Biotech Europe, Freiburg, Germany).

extract_protocol: RNA was isolated from fibroblasts using Trizol (Invitrogen, Paisley, United Kingdom) followed by RNeasy mini kit protocol (Qiagen, Hilden, Germany). Possible DNA contamination was removed using the DNA free kit (Ambion, Austin, USA). Total RNA and universal human reference RNA (Stratagene Europe, Amsterdam, The Netherlands) were amplified according to the MessageAmp II aRNA kit protocol (Ambion, Austin, USA). Total RNA and the amplified antisense RNA (aRNA) were quantified using the 2100 Bioanalyzer (Agilent, Palo Alto, USA).

tag: universal reference RNA

source_name: Scrotum cells treated with AZA, 10nM DHT for 460 hrs

growth_protocol: Fibroblasts were grown at 37 oC with 5% CO2. They were cultured in phenol red free DMEM (Gibco BRL, Germany) supplemented with 10% FBS, 100 U/ml penicillin/streptomycin, 2 mM L-Glutamine (Sigma, St. Louis, MO), and 20 mM HEPES buffer (Gibco BRL, Eggenstein, Germany). All hormone treatments were carried out with the above mentioned medium constituents but with charcoal treated 10% FBS.

treatment_protocol: ls were treated with either (1) 10 nM DHT (in ethanol) plus 2 microg/ml AZA (in acetic acid); (2) 10 nM DHT (in ethanol) plus acetic acid; (3) ethanol plus AZA (in acetic acid); and (4) ethanol plus acetic acid. DHT (Merck, Darmstadt, Germany) was dissolved in ethanol (final dilution in culture media = 1:10,000), AZA (Sigma, Taufkirchen, Germany) was dissolved in acetic acid (final dilution in culture media = 0.5%). Passage numbers were between 3 and 9 and 1 x 106 cells were seeded per culture (T-175 flasks) (day 1). Hormone stimulations started 24 hrs after seeding the cells (day 2) and were repeated once every 48 hrs for a total of 6 times (last treatment at day 14). After the final hormone stimulation, cells remained in culture for 96 hrs prior to harvesting (day 18)


title: MPNST-19_cy3


title: AM- ARD411- acetic acid, 10nM DHT (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/70856.gif
Compound Based Treatment: DHT
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.78; Parameter Scan Time = 12:01:08; Parameter PMT Volts = 535; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21164; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.72; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.78; Parameter Scan Time = 12:01:08; Parameter PMT Volts = 555; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21240; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Labia majora treated with acetic acid, 10 nM DHT for 460 hrs


title: MPNST-18_cy3


title: MPNST-16_cy3


title: AM- ARD1097- AZA, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/73999.gif
Compound Based Treatment: AZA
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.50; Parameter Scan Time = 09:54:16; Parameter PMT Volts = 680; Parameter Scan Date = 2007-05-03; Parameter Pixel Size = 10; Parameter Laser on time = 22958; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.73; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.50; Parameter Scan Time = 09:54:16; Parameter PMT Volts = 700; Parameter Scan Date = 2007-05-03; Parameter Pixel Size = 10; Parameter Laser on time = 23034; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.90; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Labia majora treated with AZA, ethanol for 460 hrs


title: MPNST-15_cy3


title: MPNST-17_cy3


title: AM- Scrotum4- acetic acid, 10nM DHT (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70649.gif
Compound Based Treatment: DHT
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.65; Parameter Scan Time = 12:49:51; Parameter PMT Volts = 530; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20810; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.65; Parameter Scan Time = 12:49:51; Parameter PMT Volts = 570; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20886; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.00; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Scrotum cells treated with acetic acid, 10 nM DHT for 460 hrs


title: AM- ARD411- acetic acid, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/70853.gif
Compound Based Treatment: none (solvents)
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 4680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.08; Parameter Scan Time = 11:18:58; Parameter PMT Volts = 540; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21123; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.08; Parameter Scan Time = 11:18:58; Parameter PMT Volts = 565; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21199; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.97; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Labia majora treated with acetic acid , ethanol for 460 hrs


title: AM- Scrotum15- AZA, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70770.gif
Compound Based Treatment: AZA
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.27; Parameter Scan Time = 11:12:00; Parameter PMT Volts = 555; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20764; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.27; Parameter Scan Time = 11:12:00; Parameter PMT Volts = 565; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20840; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Scrotum cells treated with AZA, ethanol for 460 hrs


title: AM- Scrotum15- acetic acid, 10nM DHT    (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70590.gif
Compound Based Treatment: DHT
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.69; Parameter Scan Time = 10:56:03; Parameter PMT Volts = 560; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20746; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.69; Parameter Scan Time = 10:56:03; Parameter PMT Volts = 565; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20822; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.98; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Scrotum cells treated with acetic acid, 10nM DHT for 460 hrs


title: AM- Scrotum15- acetic acid, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70589.gif
Compound Based Treatment: none (solvents)
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 5520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.89; Parameter Scan Time = 10:37:51; Parameter PMT Volts = 560; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20729; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.89; Parameter Scan Time = 10:37:51; Parameter PMT Volts = 565; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20805; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.96; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Scrotum cells treated with acetic acid , ethanol for 460 hrs


title: MPNST-12_cy3


title: MPNST-14_cy3


title: AM- Scrotum4- acetic acid, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70648.gif
Compound Based Treatment: none (solvents)
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.23; Parameter Scan Time = 13:04:36; Parameter PMT Volts = 530; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20824; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.23; Parameter Scan Time = 13:04:36; Parameter PMT Volts = 560; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20900; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.02; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

tag: Scrotum cells treated with acetic acid , ethanol for 460 hrs


title: AM- ARD411- AZA, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/70854.gif
Compound Based Treatment: AZA
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.72; Parameter Scan Time = 11:33:18; Parameter PMT Volts = 535; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21137; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.72; Parameter Scan Time = 11:33:18; Parameter PMT Volts = 560; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21213; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Labia majora cells treated with AZA, ethanol for 460 hrs


title: AM- ARD1097- acetic acid, 10nM DHT (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73939.gif
Compound Based Treatment: DHT
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.29; Parameter Scan Time = 10:32:54; Parameter PMT Volts = 660; Parameter Scan Date = 2007-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 22649; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.29; Parameter Scan Time = 10:32:54; Parameter PMT Volts = 690; Parameter Scan Date = 2007-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 22725; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Labia majora treated with acetic acid , DHT for 460 hrs


title: AM- ARD411- AZA, 10nM DHT (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/70855.gif
Compound Based Treatment: AZA,DHT
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.33; Parameter Scan Time = 11:48:14; Parameter PMT Volts = 535; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21151; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.33; Parameter Scan Time = 11:48:14; Parameter PMT Volts = 560; Parameter Scan Date = 2006-10-04; Parameter Pixel Size = 10; Parameter Laser on time = 21227; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.98; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Labia majora treated with AZA, 10nM DHT for 460 hrs


title: AM- ARD1097- AZA, 10nM DHT (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73938.gif
Compound Based Treatment: AZA,DHT
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 5200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.96; Parameter Scan Time = 10:19:46; Parameter PMT Volts = 660; Parameter Scan Date = 2007-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 22637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.96; Parameter Scan Time = 10:19:46; Parameter PMT Volts = 690; Parameter Scan Date = 2007-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 22713; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Labia majora cells treated with AZA, DHT for 460 hrs


title: MPNST-13_cy3


title: AM- Scrotum4- AZA, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70650.gif
Compound Based Treatment: AZA
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 13:17:16; Parameter PMT Volts = 530; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 13:17:16; Parameter PMT Volts = 560; Parameter Scan Date = 2006-09-21; Parameter Pixel Size = 10; Parameter Laser on time = 20915; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.03; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

tag: Scrotum cells treated with AZA, ethanol for 460 hrs


title: AM- ARD1097- acetic acid, ethanol (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73937.gif
Compound Based Treatment: none (solvents)
Cell Line: labia majora

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1990, 5450; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.50; Parameter Scan Time = 10:02:39; Parameter PMT Volts = 640; Parameter Scan Date = 2007-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 22620; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.72; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.50; Parameter Scan Time = 10:02:39; Parameter PMT Volts = 710; Parameter Scan Date = 2007-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 22696; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.92; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

tag: Labia majora treated with acetic acid , ethanol for 460 hrs


title: MPNST-10_cy3


title: MPNST-6_cy3


title: MPNST-9_cy3


title: Rat_Vagina_E2_6hr_rep5

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

country: USA

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RAE230B arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS1.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Rattus norvegicus

source_name: Vaginal tissue from OVX rats treated 20ug/kg 17estradiol for 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNAeasy purification was performed according to the manufacturer's instructions


title: MPNST-5_cy3

scan_protocol: Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc, Union City, CA), and image analysis was carried out using the GenePixPro v6 software (Axon Instruments).


title: MPNST-4_cy3


title: MPNST-7_cy3


title: MPNST-11_cy3


title: MPNST-3_cy3


title: MPNST-2_cy3


title: MPNST-1_cy3


title: Rat_Vagina_E2_6hr_rep3


title: Rat_Vagina_E2_6hr_rep4


title: Rat_Vagina_Veh_6hr_rep2

source_name: Vaginal tissue from OVX rats treated with vehicle for 6 hours


title: Rat_Vagina_Veh_3Days_rep2

source_name: Vaginal tissue from OVX rats treated with vehicle for 3 days


title: Rat_Vagina_Veh_6hr_rep3


title: Rat_Vagina_Veh_6hr_rep5


title: Rat_Vagina_E2_6hr_rep1


title: Rat_Vagina_E2_3Days_rep3

source_name: Vaginal tissue from OVX rats treated 20ug/kg 17estradiol for 3 days


title: Rat_Vagina_Veh_6hr_rep4


title: Rat_Vagina_Veh_3Days_rep5


title: Rat_Vagina_E2_5Days_rep5

source_name: Vaginal tissue from OVX rats treated 20ug/kg 17estradiol for 5 days


title: Rat_Vagina_Veh_3Days_rep4


title: Rat_Vagina_E2_3Days_rep5


title: Rat_Vagina_E2_3Days_rep2


title: Rat_Vagina_E2_6hr_rep2


title: Rat_Vagina_Veh_3Days_rep1


title: Rat_Vagina_E2_3Days_rep4


title: Rat_Vagina_E2_5Days_rep4


title: Rat_Vagina_Veh_6hr_rep1


title: Rat_Vagina_E2_3Days_rep1


title: Rat_Vagina_E2_5Days_rep1


title: Rat_Vagina_E2_5Days_rep3


title: Rat_Vagina_Veh_5Days_rep3

source_name: Vaginal tissue from OVX rats treated with vehicle for 5 days


title: Rat_Vagina_Veh_5Days_rep4


title: Rat_Vagina_Veh_3Days_rep3


title: Rat_Vagina_E2_6hr_rep5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RAE230A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.


title: Rat_Vagina_E2_5Days_rep2


title: MPNST-8_cy3

source_name: MPNST

source_name: Peripheral blood derived DNA


title: AM- Scrotum15- AZA, 10nM DHT (Type 2)-1

description:
Simple annotation: Skin, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70769.gif
Compound Based Treatment: AZA,DHT
Cell Line: normal scrotum

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.69; Parameter Scan Time = 11:25:15; Parameter PMT Volts = 555; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20776; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.72; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.69; Parameter Scan Time = 11:25:15; Parameter PMT Volts = 560; Parameter Scan Date = 2006-09-20; Parameter Pixel Size = 10; Parameter Laser on time = 20852; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: universal reference RNA

source_name: Scrotum cells treated with AZA, 10nM DHT for 460 hrs


title: Rat_Vagina_Veh_6hr_rep5


title: Rat_Vagina_Veh_5Days_rep5


title: Rat_Vagina_E2_6hr_rep3


title: Rat_Vagina_Veh_5Days_rep1


title: Rat_Vagina_E2_3Days_rep5


title: Rat_Vagina_Veh_6hr_rep2


title: Rat_Vagina_E2_3Days_rep3


title: Rat_Vagina_Veh_6hr_rep1


title: Rat_Vagina_E2_6hr_rep2


title: Rat_Vagina_Veh_3Days_rep2


title: Rat_Vagina_E2_6hr_rep4


title: Rat_Vagina_E2_6hr_rep1


title: Rat_Vagina_Veh_6hr_rep4


title: Rat_Vagina_E2_3Days_rep4


title: Rat_Vagina_Veh_3Days_rep5


title: Rat_Vagina_Veh_6hr_rep3


title: Rat_Vagina_E2_3Days_rep2


title: Rat_Vagina_Veh_5Days_rep2


title: Rat_Vagina_Veh_3Days_rep3


title: Rat_Vagina_E2_3Days_rep1


title: Rat_Vagina_Veh_3Days_rep1


title: Rat_Vagina_E2_5Days_rep5


title: Rat_Vagina_E2_5Days_rep4


title: Rat_Vagina_Veh_3Days_rep4


title: Rat_Vagina_E2_5Days_rep3


title: Rat_Vagina_Veh_5Days_rep3


title: Rat_Vagina_Veh_5Days_rep5


title: Rat_Vagina_Veh_5Days_rep4


title: Rat_Vagina_Veh_5Days_rep2


title: Rat_Vagina_E2_5Days_rep1


title: Rat_Vagina_Veh_5Days_rep1


title: Rat_Vagina_E2_5Days_rep2


title: Ovarian tumor sample 307

city: Groningen

first: Rudolf

middle: Stephan Nicolaas

last: Fehrmann

state: Groningen

department: Gynecologic Oncology

institute: University Medical Center Groningen

description: Channel 2 in raw data file ; Characteristics: STATUS: 0 = end of follow-up or death unrelated to ovarian cancer ;  1 = death due to ovarian cancer FUMND: Months from primary surgery SAMPLE NR: Unique RNA reference number

hyb_protocol: Protocol is available at http://microarrays.nki.nl/download/protocols/Hybridization_oligo_array_ULS_labeling_of_aRNA_2005.pdf

scan_protocol: Arrays were scanned with the Affymetrix GMS428 scanner (Affymetrix, Santa Clara, CA) and expression values were calculated by BlueFuse software (BlueGnome, Cambridge, UK).

data_processing: raw data

source_name: Advanced stage serous ovarian cancer

label_protocol: All cRNA samples (1.5 µg) were labeled with ULS-Cy5 and ULS-Cy3 label (BIOKÉ, Leiden, the Netherlands).

growth_protocol: All tumor samples were flash frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA from tumor samples was pelleted through cesium chloride density gradient ultracentrifugation (Roche, Almere, the Netherlands). After total RNA samples had been given DNAse treatment (Megascript T7 kit, Ambion, Huntingdon, UK), they were checked for residual DNA using a dinucleotide primer set D11S875 specific for genomic DNA. mRNA was linearly amplified by in vitro transcription using T7 RNA polymerase (Megascript T7 kit, Ambion, Huntingdon, UK) [13]. Quality/integrity of total and amplified mRNA (cRNA) was checked by spectrophotometer analysis, UV 260/280 ratio > 1.8, and/or agarose gel electrophoresis.

treatment_protocol: All tumor samples were obtained at primary surgery prior to chemotherapy.

tag: assigned unique patient id

tag: status

tag: fumnd

tag: age

tag: sample nr


title: Ovarian tumor sample 303


title: Ovarian tumor sample 174

description: Channel 1 in raw data file ; Characteristics: STATUS: 0 = end of follow-up or death unrelated to ovarian cancer ;  1 = death due to ovarian cancer FUMND: Months from primary surgery SAMPLE NR: Unique RNA reference number


title: Ovarian tumor sample 97


title: Ovarian tumor sample 73


title: Ovarian tumor sample 69


title: Ovarian tumor sample 411


title: Ovarian tumor sample 68


title: Ovarian tumor sample 25


title: Ovarian tumor sample 308


title: Ovarian tumor sample 410


title: Ovarian tumor sample 380


title: Ovarian tumor sample 67


title: Ovarian tumor sample 66


title: Ovarian tumor sample 33


title: Ovarian tumor sample 175


title: Ovarian tumor sample 412


title: Ovarian tumor sample 91


title: Ovarian tumor sample 266


title: Ovarian tumor sample 306


title: Ovarian tumor sample 277


title: Ovarian tumor sample 138


title: Ovarian tumor sample 109


title: Ovarian tumor sample 213


title: Ovarian tumor sample 55


title: Ovarian tumor sample 43


title: Ovarian tumor sample 54


title: Ovarian tumor sample 44


title: Ovarian tumor sample 162


title: Ovarian tumor sample 53


title: Ovarian tumor sample 65


title: Ovarian tumor sample 41


title: Ovarian tumor sample 357


title: Ovarian tumor sample 377


title: Ovarian tumor sample 252


title: Ovarian tumor sample 110


title: Ovarian tumor sample 253


title: Ovarian tumor sample 64


title: Ovarian tumor sample 242


title: Ovarian tumor sample 345


title: Ovarian tumor sample 251


title: Ovarian tumor sample 12


title: Ovarian tumor sample 93


title: Ovarian tumor sample 95


title: Ovarian tumor sample 134


title: Ovarian tumor sample 334


title: Ovarian tumor sample 415


title: Ovarian tumor sample 290


title: Ovarian tumor sample 281


title: Ovarian tumor sample 140


title: Ovarian tumor sample 71


title: Ovarian tumor sample 179


title: Ovarian tumor sample 164


title: Ovarian tumor sample 85


title: Ovarian tumor sample 299


title: Ovarian tumor sample 83


title: Ovarian tumor sample 362


title: Ovarian tumor sample 58


title: Ovarian tumor sample 356


title: Ovarian tumor sample 243


title: Ovarian tumor sample 81


title: Ovarian tumor sample 10


title: Ovarian tumor sample 207


title: Ovarian tumor sample 197


title: Ovarian tumor sample 79


title: Ovarian tumor sample 393


title: Ovarian tumor sample 347


title: Ovarian tumor sample 156


title: Ovarian tumor sample 351


title: Ovarian tumor sample 139


title: Ovarian tumor sample 399


title: Ovarian tumor sample 250


title: Ovarian tumor sample 333


title: Ovarian tumor sample 221


title: Ovarian tumor sample 130


title: Ovarian tumor sample 332


title: Ovarian tumor sample 37


title: Ovarian tumor sample 57


title: Ovarian tumor sample 343


title: Ovarian tumor sample 56


title: Ovarian tumor sample 11


title: Ovarian tumor sample 414


title: Ovarian tumor sample 144


title: Ovarian tumor sample 367


title: Ovarian tumor sample 148


title: Ovarian tumor sample 413


title: Ovarian tumor sample 279


title: Ovarian tumor sample 178


title: Ovarian tumor sample 50


title: Ovarian tumor sample 102


title: Ovarian tumor sample 188


title: Ovarian tumor sample 302


title: Ovarian tumor sample 190


title: Ovarian tumor sample 239


title: Ovarian tumor sample 101


title: Ovarian tumor sample 363


title: Ovarian tumor sample 172


title: Ovarian tumor sample 215


title: Ovarian tumor sample 143


title: Ovarian tumor sample 240


title: Ovarian tumor sample 336


title: Ovarian tumor sample 301


title: Ovarian tumor sample 158


title: Ovarian tumor sample 177


title: Ovarian tumor sample 163


title: Ovarian tumor sample 396


title: Ovarian tumor sample 262


title: Ovarian tumor sample 223


title: Ovarian tumor sample 295


title: Ovarian tumor sample 341


title: Ovarian tumor sample 298


title: Ovarian tumor sample 35


title: Ovarian tumor sample 280


title: Ovarian tumor sample 387


title: Ovarian tumor sample 376


title: Ovarian tumor sample 206


title: Ovarian tumor sample 31


title: Ovarian tumor sample 315


title: Ovarian tumor sample 325


title: Ovarian tumor sample 72


title: Ovarian tumor sample 199


title: Ovarian tumor sample 384


title: Ovarian tumor sample 249


title: Ovarian tumor sample 408


title: Ovarian tumor sample 30


title: Ovarian tumor sample 335


title: Ovarian tumor sample 294


title: Ovarian tumor sample 9


title: Ovarian tumor sample 323


title: Ovarian tumor sample 359


title: Ovarian tumor sample 184


title: Ovarian tumor sample 107


title: Ovarian tumor sample 394


title: Ovarian tumor sample 358


title: Ovarian tumor sample 409


title: Ovarian tumor sample 260


title: Ovarian tumor sample 8


title: Ovarian tumor sample 161


title: Ovarian tumor sample 395


title: Ovarian tumor sample 195


title: Ovarian tumor sample 4


title: Ovarian tumor sample 194


title: Ovarian tumor sample 305


title: Ovarian tumor sample 153


title: Ovarian tumor sample 317


title: Ovarian tumor sample 154


title: Ovarian tumor sample 146


title: Ovarian tumor sample 183


title: Ovarian tumor sample 182


title: Ovarian tumor sample 310


title: Ovarian tumor sample 321


title: Ovarian tumor sample 403


title: Ovarian tumor sample 229


title: Ovarian tumor sample 193


title: Ovarian tumor sample 145


title: Ovarian tumor sample 402


title: Ovarian tumor sample 401


title: Ovarian tumor sample 338


title: Ovarian tumor sample 320


title: Ovarian tumor sample 319


title: Ovarian tumor sample 237


title: Ovarian tumor sample 219


title: Ovarian tumor sample 292


title: Ovarian tumor sample 238


title: Ovarian tumor sample 168


title: Ovarian tumor sample 120


title: Ovarian tumor sample 2


title: Ovarian tumor sample 160


title: Ovarian tumor sample 220


title: Ovarian tumor sample 264


title: Ovarian tumor sample 272


title: Ovarian tumor sample 123


title: Ovarian tumor sample 28


title: Ovarian tumor sample 121


title: Ovarian tumor sample 29


title: Ovarian tumor sample 46


title: Ovarian tumor sample 211


title: Ovarian tumor sample 373


title: Ovarian tumor sample 187


title: Ovarian tumor sample 150


title: Ovarian tumor sample 167


title: Ovarian tumor sample 360


title: Ovarian tumor sample 52


title: Ovarian tumor sample 125


title: Ovarian tumor sample 104


title: Ovarian tumor sample 405


title: Ovarian tumor sample 406


title: Ovarian tumor sample 117


title: Ovarian tumor sample 116


title: Ovarian tumor sample 293


title: Ovarian tumor sample 349


title: Ovarian tumor sample 114


title: Ovarian tumor sample 233


title: Ovarian tumor sample 61


title: Ovarian tumor sample 316


title: Ovarian tumor sample 118


title: Ovarian tumor sample 113


title: Ovarian tumor sample 60


title: Ovarian tumor sample 155


title: Ovarian tumor sample 62


title: Ovarian tumor sample 39


title: Ovarian tumor sample 271


title: Ovarian tumor sample 115


title: Ovarian tumor sample 47


title: Ovarian tumor sample 234


title: Ovarian tumor sample 49


title: Ovarian tumor sample 48


title: Ovarian tumor sample 382


title: Ovarian tumor sample 365


title: Ovarian tumor sample 232


title: Ovarian tumor sample 27


title: Ovarian tumor sample 369


title: Ovarian tumor sample 218


title: Ovarian tumor sample 227


title: Ovarian tumor sample 331


title: Ovarian tumor sample 133


title: Ovarian tumor sample 217


title: Ovarian tumor sample 225


title: Ovarian tumor sample 210


title: Ovarian tumor sample 136


title: Ovarian tumor sample 176


title: Ovarian tumor sample 389


title: Ovarian tumor sample 77


title: Ovarian tumor sample 51


title: Ovarian tumor sample 1


title: Ovarian tumor sample 186


title: Ovarian tumor sample 226


title: Ovarian tumor sample 375


title: Ovarian tumor sample 224


title: Ovarian tumor sample 99


title: Ovarian tumor sample 324


title: Ovarian tumor sample 151


title: Ovarian tumor sample 322


title: Ovarian tumor sample 7


title: Ovarian tumor sample 350


title: Ovarian tumor sample 327


title: Ovarian tumor sample 17


title: Ovarian tumor sample 40


title: Ovarian tumor sample 76


title: Ovarian tumor sample 92


title: Ovarian tumor sample 263


title: Ovarian tumor sample 364


title: Ovarian tumor sample 276


title: Ovarian tumor sample 329


title: Ovarian tumor sample 245


title: Ovarian tumor sample 248


title: Ovarian tumor sample 398


title: High Light_9

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

description: no additional information

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.5 µg of labeled RNA.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.5.1.1 and the protocol GE1-v5_105_DEC08 for Cy3 labelled arrays.

data_processing: The medians of the raw data were quantile-normalized using the Bioconductor package “limma” .

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis PCC6803 culture raised under high light conditions

label_protocol: The RNA  was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Standard growth conditions: Liquid cultures of Synechocystis 6803 were grown at 30°C in BG11 (20mM TES pH 7.6) medium under continuous illumination with white light of 50 μmol of photons•m–2•s–1 and a continuous stream of air.

extract_protocol: Synechocystis 6803 cells were collected by rapid filtration (Pall Supor 800 Filter, 0,8 µm). Filters with cells were dissolved in 1 ml TRIzol (Invitrogen) per 40 ml culture, immediately frozen in liquid nitrogen and incubated 15 min at 65 °C in a water bath. Further RNA isolation followed the manufacturer’s protocol.

treatment_protocol: Different stress conditions were applied to exponentially growing cultures of Synechocystis 6803 as follows: For high light stress, light intensity was shifted from 50 to 500 μmol of photons•m–2•s–1 for 30min. Another culture was harvested after 1 h incubation in the dark. For CO2-depletion culture was centrifuged and washed one time with BG11 (20mM TES pH 7.0) w/o NaCO2. Culture was harvested after 6h in the CO2 depletion medium without a stream of air.

tag: stress

value: High Light


title: CO2-Depletion_10

description: no additional information

source_name: Synechocystis PCC6803 culture raised under CO2-depleted conditions


title: CO2-Depletion_11

description: no additional information


title: Ovarian tumor sample 6


title: Ovarian tumor sample 159


title: Ovarian tumor sample 397


title: CO2-Depletion_12

description: no additional information


title: Ovarian tumor sample 149


title: Ovarian tumor sample 342


title: High Light_8

description: no additional information


title: Control_3

description: no additional information

source_name: Synechocystis PCC6803 culture raised under control conditions

value: Control


title: High Light_7

description: no additional information


title: Ovarian tumor sample 313


title: Ovarian tumor sample 314


title: Ovarian tumor sample 5


title: Control_2

description: no additional information


title: Dark_5

description: no additional information

source_name: Synechocystis PCC6803 culture raised under dark conditions

value: Dark


title: Ovarian tumor sample 288


title: Control_1

description: no additional information


title: Ovarian tumor sample 89


title: In vitro matured oocytes rep4

city: Philadelphia

first: Young

middle: Shin

last: Lee

state: PA

address: 3307 N. Broad Street AHB 557

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description: Gene expression data from in vitro matured MII-stage oocytes

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were normalized with Affymetrix Microarray Suite version 5.0 (MAS 5.0) at the mean target intensity of 150.

label: biotin

organism: Macaca mulatta

source_name: In vitro matured rhesus MII-stage oocytes

label_protocol: Total RNA from 4 MII-stage oocytes was processed through two-rounds of amplification to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

extract_protocol: Total RNA from 4 MII-stage oocytes was extracted and purified using PicoPure kit (Arcturus).

tag: In vitro maturation

tag: oocytes


title: In vitro matured oocytes rep2


title: Ovarian tumor sample 247


title: Ovarian tumor sample 45


title: Ovarian tumor sample 87


title: Ovarian tumor sample 268


title: Ovarian tumor sample 24


title: Mus musculus hematopoietic stem cell

type: SAGE

anchor: NlaIII

city: Daegu

first: Sanggyu

address: 1370 Sankyuk-dong, Bukgu

country: South Korea

institute: Kyungpook National University

description: After NlaIII digestion, 3’ cDNAs were isolated and amplified through 16-cycle PCR. SAGE tags were released from the 3’ cDNA after linker ligation. Ditags were formed, concatemerized and cloned into a pZERO vector. Sequencing reactions were performed with the ET sequencing terminator kit.

molecule: polyA RNA

organism: Mus musculus

source_name: Mus musculus, C57BL/6, Lin- c-kit+ Hematopoietic stem cell

extract_protocol: Total RNA and mRNA were purified from the purified cells using Trizol reagent and magnetic oligo dT beads.

tag: cell type

value: GSM322870 hematopoietic stem cell

tag: genetic background


title: In vitro matured oocytes rep1


title: Ovarian tumor sample 339


title: In vivo matured oocytes rep3

description: Gene expression data from in vivo matured MII-stage oocytes

source_name: In vivo matured rhesus MII-stage oocytes

tag: In vivo maturation


title: In vivo matured oocytes rep2


title: In vivo matured oocytes rep1


title: Ovarian tumor sample 340


title: Ovarian tumor sample 214


title: Ovarian tumor sample 157


title: Ovarian tumor sample 355


title: Ovarian tumor sample 283


title: Ovarian tumor sample 88


title: Ovarian tumor sample 3


title: Ovarian tumor sample 212


title: Ovarian tumor sample 258


title: Ovarian tumor sample 259


title: In vitro matured oocytes rep3


title: Ovarian tumor sample 108


title: Dark_6

description: no additional information


title: Ovarian tumor sample 328


title: Ovarian tumor sample 32


title: Ovarian tumor sample 297


title: Ovarian tumor sample 371


title: Ovarian tumor sample 354


title: Ovarian tumor sample 287


title: Ovarian tumor sample 312


title: Ovarian tumor sample 132


title: Ovarian tumor sample 222


title: Ovarian tumor sample 246


title: Ovarian tumor sample 361


title: In vivo matured oocytes rep4


title: Ovarian tumor sample 392


title: Ovarian tumor sample 152


title: Ovarian tumor sample 311


title: Ovarian tumor sample 16


title: Ovarian tumor sample 261


title: Ovarian tumor sample 42


title: Ovarian tumor sample 391


title: Ovarian tumor sample 128


title: Ovarian tumor sample 26


title: Ovarian tumor sample 228


title: Ovarian tumor sample 407


title: Ovarian tumor sample 36


title: Dark_4

description: no additional information


title: Ovarian tumor sample 372


title: Ovarian tumor sample 216


title: Ovarian tumor sample 275


title: Ovarian tumor sample 82


title: Ovarian tumor sample 318


title: Ovarian tumor sample 209


title: Ovarian tumor sample 374


title: Ovarian tumor sample 278


title: Ovarian tumor sample 170


title: Ovarian tumor sample 59


title: Ovarian tumor sample 353


title: Ovarian tumor sample 236


title: Ovarian tumor sample 135


title: Ovarian tumor sample 181


title: Ovarian tumor sample 205


title: Ovarian tumor sample 124


title: Ovarian tumor sample 368


title: Ovarian tumor sample 204


title: Ovarian tumor sample 291


title: Ovarian tumor sample 203


title: Ovarian tumor sample 337


title: Ovarian tumor sample 286


title: Ovarian tumor sample 20


title: Ovarian tumor sample 122


title: Ovarian tumor sample 23


title: Ovarian tumor sample 173


title: Ovarian tumor sample 285


title: Ovarian tumor sample 284


title: Ovarian tumor sample 22


title: Ovarian tumor sample 19


title: Ovarian tumor sample 129


title: Ovarian tumor sample 383


title: Ovarian tumor sample 86


title: MKN74 cell_glucose free medium_18h

city: Ariake

first: Akihiro

last: Tomida

state: Koto-ku, Tokyo

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research (JFCR)

description: MKN74 cell_glucose free medium_18h

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized by the Robust Multichip Average (RMA) methods using the RMAExpress version 1.0.

source_name: MKN74 cell_glucose free medium_18h

label_protocol: cRNA targets for hybridization to GeneChip were prepared by reverse transcription from 5 μg of total RNA and then labeled with biotin according to standard Affymetrix protocols.

growth_protocol: Cells were maintained in PRIM1640 (HT-29, HT1080 and MKN74HT-29) or DMEM (HeLa), containing 2mg/mL of glucose, supplemented with with 10% FBS and 100 μg/mL of kanamycin, and cultured at 37°C , 5% CO2 as the normal growth condition.

extract_protocol: Total RNA from cultured cells was isolated using the RNeasy RNA purification kit (Qiagen, CA, USA) according to the manufacturer's instructions.

treatment_protocol: To induce the UPR, we treated cells (HeLa, HT-29, HT1080, MKN74) for 15 or 18 hours under ER stress conditions by replacing the medium with glucose-free medium or by adding either 2-Deoxy-D-glucose (2DG) or Tunicamycin (TM) to glucose-containing medium. UPR modulators (VST, biguanides or pyrvinium pamoate) were added at various final concentrations immediately after cells were placed in glucose-free medium or just before the chemical stressors were added to glucose-containing culture medium.

tag: cancer cell line

tag: MKN74 stomach cancer cell


title: Ovarian tumor sample 270


title: MKN74 cell_glucose free medium_1μM VST_18h


title: MKN74 cell_normal growth condition_1μM VST_18h


title: HT1080 cell_5μg/mL tunicamycin_3μM VST_18h

tag: HT1080 fibrosarcoma cell


title: MKN74 cell_normal growth condition_18h

description: MKN74 cell_normal growth condition_18h

source_name: MKN74 cell_normal growth condition_18h


title: Ovarian tumor sample 202


title: Ovarian tumor sample 100


title: HT1080 cell_5μg/mL tunicamycin_18h

description: HT1080 cell_5μg/mL tunicamycin_18h

source_name: HT1080 cell_5μg/mL tunicamycin_18h


title: Ovarian tumor sample 166


title: HT1080 cell_10mM 2-deoxyglucose_0.1μM pyrvinium pamoate_18h


title: HT1080 cell_10mM 2-deoxyglucose_100μM phenformin_18h


title: Ovarian tumor sample 80


title: Ovarian tumor sample 235


title: Ovarian tumor sample 165


title: HT1080 cell_10mM 2-deoxyglucose_3μM VST_18h


title: Ovarian tumor sample 147


title: HT1080 cell_10mM 2-deoxyglucose_18h_rep#2

source_name: HT1080 cell_10mM 2-deoxyglucose_18h


title: HT1080 cell_10mM 2-deoxyglucose_300μM buformin_18h


title: Ovarian tumor sample 255


title: HT1080 cell_10mM 2-deoxyglucose_10mM metformin_18h


title: Ovarian tumor sample 105


title: Ovarian tumor sample 366


title: Ovarian tumor sample 38


title: HT1080 cell_glucose free medium_18h

description: HT1080 cell_glucose free medium_18h

source_name: HT1080 cell_glucose free medium_18h


title: HT1080 cell_normal growth condition_0.1μM pyrvinium pamoate_18h


title: HT1080 cell_10mM 2-deoxyglucose_18h_rep#1


title: Ovarian tumor sample 189


title: Ovarian tumor sample 21


title: HT1080 cell_normal growth condition_100μM phenformin_18h


title: HT1080 cell_normal growth condition_10mM metformin_18h


title: HT1080 cell_glucose free medium_3μM VST_18h


title: Ovarian tumor sample 106


title: HT1080 cell_normal growth condition_300μM buformin_18h


title: Ovarian tumor sample 75


title: Ovarian tumor sample 78


title: Ovarian tumor sample 244


title: HT1080 cell_normal growth condition_18h_rep#3

source_name: HT1080 cell_normal growth condition_18h


title: HT1080 cell_normal growth condition_18h_rep#4


title: Ovarian tumor sample 346


title: Ovarian tumor sample 386


title: HT-29 cell_glucose free medium_18h_rep#1

source_name: HT-29 cell_glucose free medium_18h

tag: HT-29 colon cancer cell


title: HT1080 cell_normal growth condition_18h_rep#1


title: HT1080 cell_normal growth condition_18h_rep#2


title: HT-29 cell_normal growth condition_18h_rep#2

source_name: HT-29 cell_normal growth condition_18h


title: HT-29 cell_glucose free medium_10μM VST_18h


title: Ovarian tumor sample 257


title: Ovarian tumor sample 289


title: Ovarian tumor sample 385


title: Ovarian tumor sample 126


title: HT-29 cell_normal growth condition_10μM VST_18h


title: Ovarian tumor sample 185


title: HT-29 cell_glucose free medium_18h_rep#2


title: Ovarian tumor sample 269


title: Ovarian tumor sample 127


title: HT1080 cell_normal growth condition_3μM VST_18h


title: HT-29 cell_normal growth condition_18h_rep#1


title: Ovarian tumor sample 192


title: Ovarian tumor sample 241


title: HeLa cell_5mM 2-deoxyglucose_1μM VST_18h

tag: HeLa epithelial carcinoma cell


title: Ovarian tumor sample 103


title: Ovarian tumor sample 282


title: HeLa cell_1μg/mL tunicamycin_18h

description: HeLa cell_1μg/mL tunicamycin_18h

source_name: HeLa cell_1μg/mL tunicamycin_18h


title: HeLa cell_glucose free medium_15μM phenformin_15h


title: HeLa cell_5mM 2-deoxyglucose_18h

description: HeLa cell_5mM 2-deoxyglucose_18h

source_name: HeLa cell_5mM 2-deoxyglucose_18h


title: HeLa cell_glucose free medium_1.5mM metformin_15h


title: HeLa cell_glucose free medium_50μM buformin_15h


title: Ovarian tumor sample 309

source_name: Advanced stage serous ovarian cancer


title: Ovarian tumor sample 265


title: Ovarian tumor sample 34


title: Ovarian tumor sample 94


title: Ovarian tumor sample 18


title: Ovarian tumor sample 196


title: Ovarian tumor sample 84


title: HeLa cell_glucose free medium_18h

description: HeLa cell_glucose free medium_18h

source_name: HeLa cell_glucose free medium_18h


title: HeLa cell_glucose free medium_15h

description: HeLa cell_glucose free medium_15h

source_name: HeLa cell_glucose free medium_15h


title: HeLa cell_normal growth condition_15h

description: HeLa cell_normal growth condition_15h

source_name: HeLa cell_normal growth condition_15h


title: HeLa cell_glucose free medium_1μM VST_18h


title: HeLa cell_normal growth condition_1μM VST_18h


title: Ovarian tumor sample 142


title: HeLa cell_normal growth condition_18h

description: HeLa cell_normal growth condition_18h

source_name: HeLa cell_normal growth condition_18h


title: Ovarian tumor sample 119


title: Ovarian tumor sample 112


title: K562_ICL670_50uM_dup2

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

description: Description Effect of ICL670 in K562 cells

hyb_protocol: GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Hybridization Oven 640 110V (Affymetrix 800138) Wash and staining: Fluidics Station 450 (Affymetrix 00-0079)

scan_protocol: GeneChip Scanner 3000 (Affymetrix 00-0074) GeneChip Operating Software ver.1.4 (Affymetrix 690036)

data_processing: Data Processing GeneChip Operating Software ver.1.4 (Affymetrix 690036)

source_name: ICL670 50uM 16hrs

label_protocol: One-cycle Target Labeling GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Section 2 Eukaryotic Sample and Array processing Chapter 1 Eukaryotic Target Prepartion

extract_protocol: RNeasy kit

tag: ICL670 50uM 16hrs, K562 cells


title: Ovarian tumor sample 379

tag: assigned unique patient id


title: Ovarian tumor sample 201

tag: status


title: Ovarian tumor sample 131

tag: fumnd


title: K562_ICL670_untreated_dup1

source_name: Mock

treatment_protocol: Mock

tag: Human myeloid leukemia cell line


title: Ovarian tumor sample 378

tag: age

tag: sample nr


title: K562_ICL670_10uM_dup2

source_name: ICL670-treated K562 cells

tag: ICL670 10uM for 16hrs


title: K562_ICL670_50uM_dup1


title: Ovarian tumor sample 180


title: Vaginal_Control_Donor16

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 2.0 Plus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: Vaginal tissue from subjects prior to treatment

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNAeasy purificition was performed according to the manufacturer's instructions

tag: Age

tag: BMI

tag: Ethnic Origin

value: White


title: Vaginal_Control_Donor19


title: Ovarian tumor sample 15


title: Ovarian tumor sample 267


title: Ovarian tumor sample 111


title: Vaginal_Control_Donor17


title: K562_ICL670_10uM_dup1

source_name: ICL670 10uM for 16hs

tag: ICL670 treated K562 cells (10uM for 16hrs)


title: Ovarian tumor sample 344


title: Ovarian tumor sample 400


title: Ovarian tumor sample 90


title: Vaginal_Control_Donor14


title: K562_ICL670_untreated_dup2


title: Ovarian tumor sample 96


title: Vaginal_Control_Donor15


title: Vaginal_Control_Donor18


title: Vaginal_Control_Donor13

value: Black or African American


title: BRR2 (Cy5) vs. brr2-Dsec63 (Cy3) at 16C for 10 min

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: A complete description of the protocols used can be found in manuscript.

hyb_protocol: Competitive hybridization at 60C for 16hours

scan_protocol: Images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 6.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global LOWESS regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

label_protocol: Aminoallyl dUTP incorporation in cDNA reaction, followed by coupling to NHS-ester

extract_protocol: Phenol Extraction

tag: genotype

tag: condition

tag: time

extract_protocol: Phenol extraction


title: Ovarian tumor sample 254


title: Vaginal_Control_Donor12


title: brr2-Dsec63 (Cy5) vs. BRR2 (Cy3) at 16C for 10 min


title: BRR2 (Cy5) vs. brr2-1 (Cy3) at 16C for 10 min


title: Vaginal_Control_Donor10


title: Vaginal_Control_Donor11


title: piPSC, biological replicate 2

city: La Jolla

first: Hongyan

last: Zhou

state: CA

address: 10550 North Torrey Pines Road

institute: the scripps research institute

description: Gene expression data from mouse piPS cells

hyb_protocol: The hybridization mix containing 750 ng of labeled amplified cRNA was prepared according to the Illumina BeadStation 500X System Manual (Illumina, San Diego, CA, USA) using the supplied reagents and GE Healthcare Streptavidin-Cy3 staining solution. Hybridization to the Illumina Array MouseRef-8 v2 was for 18 h at 55 °C on a BeadChip Hyb Wheel.

scan_protocol: The array was scanned using the Illumina BeadArray Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.

source_name: piPSC

label_protocol: Biotin-16-UTP-labeled cRNA was synthesized from 500 ng total RNA with the  Illumina TotalPrep RNA amplification kit (Ambion AMIL1791, Foster City, CA, USA).

growth_protocol: ES cells were cultured at 37°C with 5% CO2. mES cells were maintained on irradiated MEF feeders in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 10% fetal bovine serum (FBS; GIBCO), 0.1 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, and 1,000 units/ml of LIF (Chemicon).

extract_protocol: Total RNA was extracted and purified with RNeasy Plus minikit (Qiagen).

tag: cell type

value: protein induced pluripotent stem cells


title: Ovarian tumor sample 208


title: brr2-1 (Cy5) vs. BRR2 (Cy3) at 16C for 10 min


title: Ovarian tumor sample 296


title: Ovarian tumor sample 348


title: OG2-MEF, biological replicate 2

description:
Oct4-GFP transgenic mice were from the Jackson Laboratory. OG2-GFP MEFs were prepared from E13.5 embryos.
Gene expression data from MEF cells

source_name: mouse embryonic fibroblast (MEF) haboring the GFP transgene driven by Oct4 promoter.

growth_protocol: OG2-MEFs were cultured on gelatin-coated dishes in normal MEF media: high-glucose D-MEM  (Invitrogen) with 10% FBS, 0.1 mM non-essential amino acids, and 2 mM L-glutamine.

value: OG2-GFP MEFs prepared from E13.5 embryos


title: ES cells, biological replicate 2

description: Gene expression data from mouse ES cells

source_name: R1 mouse embryonic stem (ES) cells

value: R1 mouse ES cells


title: Vaginal_Control_Donor9


title: ES cells, biological replicate 1


title: Vaginal_Control_Donor8


title: Ovarian tumor sample 274


title: Ovarian tumor sample 200


title: OG2-MEF, biological replicate 1

value: OG2-GFP MEFs prepared from E13.5 embryos.


title: Vaginal_Control_Donor6


title: Ovarian tumor sample 14


title: Vaginal_Control_Donor7


title: piPSC, biological replicate 1


title: Ovarian tumor sample 98


title: Ovarian tumor sample 63


title: pCREB, cocaine treatment, replicate 3

city: Dallas

first: guanghua

last: xiao

state: TX

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: University of Texas Southwestern Medical Center

hyb_protocol: NimbleGen standard protocol. Samples of Cy5-labeled immunoprecipitated DNA and Cy3-labeled input DNA were mixed and hybridized to NimbleGen (Madison, WI) MM8 mouse promoter microarrays.

scan_protocol: NimbleGen standard protocol.

data_processing: The log2 ratios of signal intensities between the immunoprecipitated samples and control genomic DNA (input).These ratios were scaled by Tukey's Bi-weight method.

source_name: pCREB immunoprecipitation, cocaine

label_protocol: NimbleGen standard protocol.

extract_protocol: Fresh nucleus accumbens (NAc) punches were cross-linked and lysed, and the chromatin was fragmented by sonication to an average length of 700 bp. For each sample, bilateral NAc punches were pooled from ~8 mice. Aliquots of sonicated chromatin were incubated with 4 µg of the following polyclonal antibodies for 8 hr at 4°C: anti-dimethyl K9/K27 H3  (cat. #ab7312, Abcam, Cambridge, UK); anti-FosB(C-terminus) antibody generated at UT Southwestern; anti-pan FosB/deltaFosB (cat. #SC-048, Santa Cruz Biotechnology, Santa Cruz, CA); and anti-phospho-CREB (cat. #06-519, Upstate). Note that for deltaFosB ChIP, chromatin was first immunoprecipitated with anti-FosB (C-terminus) to precipitate any full-length FosB-bound chromatin, followed by anti-pan FosB/deltaFosB which then precipitates deltaFosB-bound chromatin. These conditions have been shown to selectively precipitate deltaFosB-bound chromatin (Kumar et al., Neuron 2005). Immunprecipitates were reverse cross-linked, and both the immunoprecipitated (enriched) and total (input or non-enriched) DNA from each treatment group was amplified and labeled with a fluorescent dye (Cy5 and Cy3) with the use of ligation-mediated-polymerase chain reaction (Sikder et al., JBC 2006).

treatment_protocol: 7 days of saline or cocaine (20mg/kg).

tag: antibody

value: anti-phospho-CREB

tag: strain

tag: gender

value: male

value: 10-12 weeks

tag: tissue

value: brain

tag: brain region

value: nucleus accumbens

tag: treatment

value: cocaine

source_name: input


title: Ovarian tumor sample 74

tag: assigned unique patient id

tag: status

tag: fumnd

tag: age


title: Ovarian tumor sample 273

tag: sample nr


title: Ovarian tumor sample 13


title: Vaginal_Control_Donor5

tag: Age

tag: BMI

tag: Ethnic Origin


title: pCREB, saline treatment, replicate 2

source_name: pCREB immunoprecipitation, saline

value: saline


title: Vaginal_Control_Donor2


title: Vaginal_Control_Donor3

value: American Indian or Alaska Native


title: Vaginal_Control_Donor1


title: Ovarian tumor sample 352


title: Ovarian tumor sample 388


title: Vaginal_Control_Donor4


title: pCREB, cocaine treatment, replicate 1


title: pCREB, cocaine treatment, replicate 2


title: DeltaFosB, cocaine treatment, replicate 3

source_name: deltaFosB immunoprecipitation, cocaine

value: anti-FosB followed by anti-pan FosB/deltaFosB


title: Vaginal_E2_Donor18

source_name: Vaginal tissue from subjects treated for 3 months with 17b-estradiol, delivered via a skin patch, at a dose of 0.05 mg/day


title: Vaginal_E2_Donor19


title: Ovarian tumor sample 381

source_name: Advanced stage serous ovarian cancer


title: Vaginal_E2_Donor17


title: DeltaFosB, saline treatment, replicate 3

source_name: deltaFosB immunoprecipitation, saline


title: DeltaFosB, cocaine treatment, replicate 2


title: pCREB, saline treatment, replicate 1


title: Vaginal_E2_Donor16


title: DeltaFosB, cocaine treatment, replicate 1


title: pCREB, saline treatment, replicate 3


title: Ovarian tumor sample 230


title: Ovarian tumor sample 231


title: Ovarian tumor sample 137


title: DeltaFosB, saline treatment, replicate 2


title: Vaginal_E2_Donor14


title: Ovarian tumor sample 141


title: Ovarian tumor sample 191


title: Vaginal_E2_Donor11


title: histone H3K9/27 methylation, cocaine treatment, replicate 1

source_name: H3K9/27 immunoprecipitation, cocaine

value: anti-dimethyl K9/K27 H3


title: DeltaFosB, saline treatment, replicate 1


title: Ovarian tumor sample 304


title: histone H3K9/27 methylation, cocaine treatment, replicate 2


title: Vaginal_E2_Donor15


title: Vaginal_E2_Donor12


title: Ovarian tumor sample 404


title: Vaginal_E2_Donor9


title: Vaginal_E2_Donor13


title: histone H3K9/27 methylation, saline treatment, replicate 2

source_name: H3K9/27 immunoprecipitation, saline


title: Ovarian tumor sample 370


title: Vaginal_E2_Donor10


title: histone H3K9/27 methylation, saline treatment, replicate 1


title: histone H4 acetylation, saline treatment, replicate 2

hyb_protocol: NimbleGen standard protocol. Samples of Cy5-labeled immunoprecipitated DNA and Cy3-labeled input DNA were mixed and hybridized to NimbleGen (Madison, WI) MM5 mouse promoter microarrays.

source_name: AcH4 immunoprecipitation, saline

extract_protocol: Fresh nucleus accumbens (NAc) punches were cross-linked and lysed, and the chromatin was fragmented by sonication to an average length of 700 bp. For each sample, bilateral NAc punches were pooled from ~8 mice. Aliquots of sonicated chromatin were incubated with 4 µg of the following polyclonal antibodies for 8 hr at 4°C: anti-acetylated K9/K14 H3 (cat. #06-599, Upstate/Millipore, Billerica, MA,) or anti-acetylated K5/K8/K12/K16 H4 (cat. #06-866, Upstate). Immunprecipitates were reverse cross-linked, and both the immunoprecipitated (enriched) and total (input or non-enriched) DNA from each treatment group was amplified and labeled with a fluorescent dye (Cy5 and Cy3) with the use of ligation-mediated-polymerase chain reaction (Sikder et al., JBC 2006).

value: anti-acetylated K5/K8/K12/K16 H4


title: histone H4 acetylation, cocaine treatment, replicate 2

source_name: AcH4 immunoprecipitation, cocaine


title: Ovarian tumor sample 256


title: histone H3 acetylation, cocaine treatment, replicate 2

source_name: AcH3 immunoprecipitation, cocaine

value: anti-acetylated K9/K14 H3


title: Vaginal_E2_Donor7

value: White


title: Ovarian tumor sample 326


title: Vaginal_E2_Donor6


title: Ovarian tumor sample 300


title: Vaginal_E2_Donor8


title: Ovarian tumor sample 171


title: histone H3 acetylation, saline treatment, replicate 2

source_name: AcH3 immunoprecipitation, saline


title: histone H4 acetylation, saline treatment, replicate 1


title: histone H4 acetylation, cocaine treatment, replicate 1


title: Vaginal_E2_Donor5


title: Vaginal_E2_Donor3


title: Ovarian tumor sample 198


title: Ovarian tumor sample 70


title: histone H3 acetylation, saline treatment, replicate 1


title: Ovarian tumor sample 390


title: Vaginal_E2_Donor4

value: Black or African American


title: SGF3165_FLAG_MES4FLAG_EEMB_2 extraction1_array1

status: Public on May 19 2009

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: lab: Strome; short description: An mouse monoclonal antibody to FLAG obtained from SIGMA; used to ChIP MES-4; lot: 065K6236; catalog: SGF3165; company: Other; clonal: Monoclonal; purified: Protein A/G; antigen: DYKDDDDK; host: Mouse; species: C. elegans; target name: FLAG; aliases: SGF3165_FLAG; official name: SGF3165_FLAG;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is WS180

label: Cy3 dye

organism: Caenorhabditis elegans

source_name: SGF3165_FLAG_MES4FLAG_EEMB_2 channel_1

growth_protocol: Worm_embryo_growth_and_harvest_vSS1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 4 times on ice at the following settings: 30 sec; 20% power output; 0.7 duty cycle. Cell debris was removed by centrifuging at 13,000rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000rpm, 4?C for 1 minute to remove lipids.  Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS1. Protein A or G-coupled Dynal magnetic beads from 20 ul of slurry were washed 3 times in 1ml of 5mg/ml IgG-Free BSA in PBS (wash buffer). Beads were resuspended in 100ul of the wash buffer and rotated with 5ug of the appropriate antibody overnight at 4 oC. Beads were further washed 2 times in the wash buffer and resuspended in 30ul of the wash buffer. Before beginning IP, 5% of starting material of protein (3-6mg) was saved as "input" at -20 oC. The antibody-conjugated Dynal beads were mixed with 3-6mg of protein and nutated for 2hrs at 4 oC. After washing the beads, captured proteins were eluted by incubating beads in 300 ul of TE with 1% SDS and 250mM NaCl for 2 times 15 minutes at 65 oC. Samples were treated with proteinase K and reverse-crosslinked at 65 oC overnight. DNA was purified using Zymo DNA purification column and eluted in in 43ul dH2O. RNA was digest for 1 hour at 37 oC with RNase One (Promega). For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn:  http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

tag: developmental stage

value: embryo

label: Cy5 dye

source_name: SGF3165_FLAG_MES4FLAG_EEMB_2 channel_2

value: SGF3165 FLAG


title: Vaginal_E2_Donor2


title: histone H3 acetylation, cocaine treatment, replicate 1


title: SGF3165_FLAG_MES4FLAG_EEMB_3 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: lab: Strome; short description: An mouse monoclonal antibody to FLAG obtained from SIGMA; used to ChIP MES-4; lot: 065K6236; catalog: SGF3165; company: Other; clonal: Monoclonal; purified: Protein A/G; antigen: DYKDDDDK; host: Mouse; species: C. elegans; target name: FLAG; aliases: SGF3165_FLAG; official name: SGF3165_FLAG;

This is a Dye Swap sample.

source_name: SGF3165_FLAG_MES4FLAG_EEMB_3 channel_1

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

source_name: SGF3165_FLAG_MES4FLAG_EEMB_3 channel_2


title: JL00003_DPY26_N2_MXEMB_3 extraction2_array0

description:
channel ch1 is ChIP DNA; Antibody information listed below: lab: Lieb; short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.; catalog: Jason Lieb; company: Covance; clonal: Polyclonal; purified: Affinity; antigen: 740-1262; host: Rabbit; species: C. elegans; target id: dpy-26; target name: DPY-26; aliases: DPY26; official name: JL0004_DPY26;
channel ch2 is input DNA;

data_processing: ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes. Processed data are obtained using following parameters: genome version is WS180

source_name: JL00003_DPY26_N2_MXEMB_3 [ChIP DNA]

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSE1. Embryos were resuspended in FA buffer and dounced 30 times (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

source_name: JL00003_DPY26_N2_MXEMB_3 [input DNA]


title: SGF3165_FLAG_MES4FLAG_EEMB_3 extraction2_array2


title: SGF3165_FLAG_MES4FLAG_EEMB_2 extraction1_array0

description:
channel ch1 is ChIP DNA; Antibody information listed below: lab: Strome; short description: An mouse monoclonal antibody to FLAG obtained from SIGMA; used to ChIP MES-4; lot: 065K6236; catalog: SGF3165; company: Other; clonal: Monoclonal; purified: Protein A/G; antigen: DYKDDDDK; host: Mouse; species: C. elegans; target name: FLAG; aliases: SGF3165_FLAG; official name: SGF3165_FLAG;
channel ch2 is input DNA;

tag: genotype

value: mes-4(bn73); bnIs15

tag: transgene

value: mes-3 promoter


title: JL00003_DPY26_N2_MXEMB_2 extraction1_array0

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: lab: Lieb; short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.; catalog: Jason Lieb; company: Covance; clonal: Polyclonal; purified: Affinity; antigen: 740-1262; host: Rabbit; species: C. elegans; target id: dpy-26; target name: DPY-26; aliases: DPY26; official name: JL0004_DPY26;

This is a Dye Swap sample.

source_name: JL00003_DPY26_N2_MXEMB_2 [input DNA]

tag: antibody

source_name: JL00003_DPY26_N2_MXEMB_2 [ChIP DNA]


title: SGF3165_FLAG_MES4FLAG_EEMB_2 extraction1_array2

tag: strain